Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Cell Line, Tumor: A cell line derived from cultured tumor cells.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Mice, Inbred C57BLPlasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Ribonuclease III: An endoribonuclease that is specific for double-stranded RNA. It plays a role in POST-TRANSCRIPTIONAL RNA PROCESSING of pre-RIBOSOMAL RNA and a variety of other RNA structures that contain double-stranded regions.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.RNA, Small Nucleolar: Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Bacterial Proteins: Proteins found in any species of bacterium.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Genes, Plant: The functional hereditary units of PLANTS.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Argonaute Proteins: A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Viral Proteins: Proteins found in any species of virus.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.RNA, Neoplasm: RNA present in neoplastic tissue.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Genes, Viral: The functional hereditary units of VIRUSES.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 220.127.116.11.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Disease Models, Animal: Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Epithelial Cells: Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Immediate-Early Proteins: Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Kinetics: The rate dynamics in chemical or physical systems.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.Recombinant Proteins: Proteins prepared by recombinant DNA technology.RNA, Guide: Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.RNA, Catalytic: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Genes, Immediate-Early: Genes that show rapid and transient expression in the absence of de novo protein synthesis. The term was originally used exclusively for viral genes where immediate-early referred to transcription immediately following virus integration into the host cell. It is also used to describe cellular genes which are expressed immediately after resting cells are stimulated by extracellular signals such as growth factors and neurotransmitters.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Microdissection: The performance of dissections with the aid of a microscope.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.RNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Rats, Wistar: A strain of albino rat developed at the Wistar Institute that has spread widely at other institutions. This has markedly diluted the original strain.RNA-Induced Silencing Complex: A multicomponent, ribonucleoprotein complex comprised of one of the family of ARGONAUTE PROTEINS and the "guide strand" of the one of the 20- to 30-nucleotide small RNAs. RISC cleaves specific RNAs, which are targeted for degradation by homology to these small RNAs. Functions in regulating gene expression are determined by the specific argonaute protein and small RNA including siRNA (RNA, SMALL INTERFERING), miRNA (MICRORNA), or piRNA (PIWI-INTERACTING RNA).Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Tumor Necrosis Factor-alpha: Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Breast Neoplasms: Tumors or cancer of the human BREAST.Gene Transfer Techniques: The introduction of functional (usually cloned) GENES into cells. A variety of techniques and naturally occurring processes are used for the gene transfer such as cell hybridization, LIPOSOMES or microcell-mediated gene transfer, ELECTROPORATION, chromosome-mediated gene transfer, TRANSFECTION, and GENETIC TRANSDUCTION. Gene transfer may result in genetically transformed cells and individual organisms.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Genes, Bacterial: The functional hereditary units of BACTERIA.
Winkler WC, Breaker RR (2005). "Regulation of bacterial gene expression by riboswitches". Annu. Rev. Microbiol. 59: 487-517. ... RNA. 15 (11): 2046-56. doi:10.1261/rna.1824209. PMC 2764483 . PMID 19776155. Retrieved 2010-08-20. Kazanov MD, Vitreschak AG, ... October 2004). "A glycine-dependent riboswitch that uses cooperative binding to control gene expression". Science. 306 (5694): ... This regulation controls parts of the sulfur metabolism of marine bacteria. SAM-I riboswitch SAM-II riboswitch SAM-III ...
AsRNAs can be involved in this level of gene regulation. For example, in bacterial or eukaryotic cells where complex RNA ... gene. FLC gene in Arabidopsis thaliana encodes for a transcription factor that prevent expression of a range of genes that ... RNA I and RNA II forms a duplex which introduces a conformational change of RNA II. Consequently, RNA II cannot hybridize with ... Epigenetic regulations such as DNA methylation and histone methylation can repress gene expression by inhibiting initiation of ...
"The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development. 16 (20): 2583- ... Kortmann J, Narberhaus F (March 2012). "Bacterial RNA thermometers: molecular zippers and switches". Nature Reviews. ... mRNA Other Regulation of gene expression cis-regulatory module Gene regulatory network Operon Promoter Trans-acting factor Rfam ... Platt T (1986). "Transcription termination and the regulation of gene expression". Annual Review of Biochemistry. 55: 339-72. ...
... as major players in post-transcriptional regulation of gene expression in response to environmental stimuli. The α-subdivision ... Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit Rev Biochem Mol Biol. 40 (2): 93-113. ... Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which ... Post-genomic research has rendered bacterial small non-coding RNAs (sRNAs) ...
"Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology. 339 (2): ... "A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase". Science. 262 (5138): ... RNA polymerase III: transcribes genes encoding transfer RNA, 5s ribosomal RNAs and other small RNAs ... 5.8S and 28S ribosomal RNAs. *RNA polymerase II: transcribes genes encoding messenger RNA and certain small nuclear RNAs and ...
Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory ... it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter ... drives expression of downstream reporter genes. This reporter region facilitates both positive and negative selection by HIS3 ... bait-prey binding must be of high enough stringency to drive reporter gene expression (HIS3) at a sufficient level to overcome ...
... for the discovery of covalent modifications of histone proteins and their critical roles in the regulation of gene expression ... for the discovery of a new world of genetic regulation by microRNAs, a class of tiny RNA molecules that inhibit translation or ... for harnessing an ancient mechanism of bacterial immunity into a powerful and general technology for editing genomes, with wide ... Charles L. Sawyers (Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center), for cancer genes and targeted ...
... gene expression regulation, archaeal MeSH G05.315.300 --- gene expression regulation, bacterial MeSH G05.315.310 --- gene ... gene expression regulation, viral MeSH G05.315.410 --- gene silencing MeSH G05.315.410.790 --- rna interference MeSH G05.315. ... gene expression regulation, fungal MeSH G05.315.370 --- gene expression regulation, neoplastic MeSH G05.315.370.500 --- gene ... expression regulation, developmental MeSH G05.315.320 --- gene expression regulation, enzymologic MeSH G05.315.320.200 --- ...
Winkler W, Nahvi A, Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression ... "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ... The expression platform is what regulates gene expression. Expression platforms typically turn off gene expression in response ... "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ...
Tetart, F; Bouche JP (1992). "Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not ... "Division inhibition gene dicF of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes". J ... DicF RNA is a non-coding RNA that is an antisense inhibitor of cell division gene ftsZ. DicF is bound by the Hfq protein which ... Faubladier, M.; Cam, K.; Bouché, J. P. (1990). "Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence ...
2012). Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection. Caister Academic Press. ISBN ... "A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide ... telomerase RNA and Y RNAs. The miRNAs are involved in the large scale regulation of many protein coding genes, the Y RNAs are ... VegT RNA, Oskar RNA, ENOD40, p53 RNA and SR1 RNA. Bifunctional RNAs have recently been the subject of a special issue of ...
The PreQ1-I riboswitch is a cis-acting element identified in bacteria which regulates expression of genes involved in ... Like any other riboswitch, the two most common types of gene regulation mediated by preQ1 riboswitch are through transcription ... RNA. 14 (4): 685-695. doi:10.1261/rna.937308. ISSN 1355-8382. PMC 2271366 . PMID 18305186. Eichhorn, Catherine D.; Kang, ... Ligand binding to the transcriptional riboswitch in bacterial causes modification in the structure of riboswitch unit, which ...
These studies have contributed much to our understanding of the regulation of gene expression, transcription factors, and the ... While the rest of a bacterial cell may stain, the endospore is left colourless. To combat this, a special stain technique ... sigma factor subunits of RNA polymerase. Endospores of the bacterium Bacillus anthracis were used in the 2001 anthrax attacks. ... Bacterial endospores are resistant to antibiotics, most disinfectants, and physical agents such as radiation, boiling, and ...
England JC, Perchuk BS, Laub MT, Gober JW (February 2010). "Global regulation of gene expression and cell differentiation in ... Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit. Rev. Biochem. Mol. Biol. 40 (2): 93-113 ... Fröhlich KS, Vogel J (December 2009). "Activation of gene expression by small RNA". Curr. Opin. Microbiol. 12 (6): 674-82. doi: ... CrfA RNA (Caulobacter response to famine RNA) is a family of non-coding RNAs found in Caulobacter crescentus. CrfA is expressed ...
Gene regulation - some toxins act as a means of general repression of gene expression while others are more specific. Growth ... The toxic effects of the protein are neutralised by the RNA gene. One example is the ToxIN system from the bacterial plant ... Rotem, Eitan (2010). "Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence". ... February 2011). "A processed noncoding RNA regulates an altruistic bacterial antiviral system". Nat. Struct. Mol. Biol. 18 (2 ...
Expression of Smr9C in free-living bacteria was found to be growth-dependent, being the gene strongly down-regulated when ... αr9 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order ... Recent deep sequencing data further revealed up-regulation of Smr9C upon salt, acidic, cold-shock and heat shock stresses. ... Parallel studies assessed Smr9C expression in S. meliloti 1021 under different biological conditions; i.e. bacterial growth in ...
... such as long-noncoding RNA and microRNAs in gene expression regulation. Small-seq is a single-cell method that captures small ... "Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells". Nature Communications ... Standard methods such as microarrays and bulk RNA-seq analysis analyze the expression of RNAs from large populations of cells. ... Generally speaking, for a typical bulk cell RNA-sequencing (RNA-seq) experiment, ten million reads are generated and a gene ...
... is a methylated form of the DNA base cytosine that may be involved in the regulation of gene transcription. ... When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the ... After seven decades, it turned out that it is also a common feature in different RNA molecules, although the precise role is ... While trying to isolate the bacterial toxin responsible for tuberculosis, W.G. Ruppel isolated a novel nucleic acid named ...
In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit transcriptional ... This allows the sigma S factor to associate with RNA polymerase and direct the expression of the stationary genes. Although ... Paget, Mark S. (2015-06-26). "Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution". ... Studies on the Specificity and Regulation of Its Expression". PLoS ONE. 6: e19235. doi:10.1371/journal.pone.0019235. PMC ...
"Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli". J. Biol. ... "Comparative genomics boosts target prediction for bacterial small RNAs". Proc Natl Acad Sci U S A. 110 (37): E3487-E3496. doi: ... FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named ... "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli". ...
Bacterial small RNAs are involved in post-transcriptional regulation. Using deep sequencing S. coelicolor transcriptome was ... 63 small RNAs were identified. Expression of 11 of them was confirmed by Northern blot. The sRNAs were shown to be only present ... It contains 8,667,507 bp, encoding 7,825 predicted genes, including over 20 gene clusters for the synthesis of known or ... The small RNA scr5239 (Streptomyces coelicolor sRNA upstream of SCO5239) has two targets. It inhibits agarase DagA expression ...
transcriptional regulation - controlling the rate of gene transcription for example by helping or hindering RNA polymerase ... gene expression - the process by which information from a gene is used in the synthesis of a functional gene product such as a ... and activate transcription of plant genes that aid in bacterial infection. TAL effectors contain a central repeat region in ... Transcription factors use a variety of mechanisms for the regulation of gene expression. These mechanisms include: * ...
... a locus of intense activity on the molecular biology of gene expression and gene regulation. While in Paris, he met Sol ... Archaea Bacterial phyla, the major lineages of Bacteria George E. Fox Karl Stetter Norman R. Pace Otto Kandler Phylogenetics ... He was also the originator of the RNA world hypothesis in 1967, although not by that name. He held the Stanley O. Ikenberry ... Horizontal gene transfer during this era was responsible for the fast early evolution of complex biological structures. In ...
Results obtained from RNA-seq experiments revealed a complex expression pattern with a group of 22 genes having expression ... abundance and activity of this protein is influenced by hydrostatic pressure and its role is related to the regulation of genes ... nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles, 1998. 2(1): p. 1-7. ... Strain SS9 has 14 ribosomal RNA (rRNA) genes on chromosome 1, and 1 on chromosome 2; this is the largest number of rRNA genes ...
"A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ... Winkler, WC; Cohen-Chalamish S; Breaker RR (2002). "An mRNA structure that controls gene expression by binding FMN". Proc Natl ... Serganov A, Huang L, Patel DJ (2009). "Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch". Nature ... Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS (2002). "Regulation of riboflavin biosynthesis and transport genes in ...
"Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora". Molecular Biology ... RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulating gene expression in ... compact genomes and genes of bacterial origin". BMC Genomics. 16 (1): 204. doi:10.1186/s12864-015-1418-3. PMC 4487195. PMID ...
Mutations within the MCRE sequence in the 5′ flanking region abolished the effects of Sp1 on the reporter gene expression both ... flanking region of the cirp gene, and down-regulation of Sp1 had the opposite effect. ... Expression of cold-inducible RNA-binding protein (cirp, also called cirbp or hnRNP A18) is known to be induced in response to ... In stable transfectants, MCRE also enhanced the reporter gene expression at 32°C, although more copy numbers of MCRE were ...
RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence ... Gene Expression Regulation, Bacterial * Host Factor 1 Protein / metabolism* * Molecular Chaperones / metabolism* ... Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA ... The relevant RNA fragments were labelled so that changes in intra- and intermolecular RNA structures can be monitored in real ...
Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for seque … ... Gene Expression Regulation, Bacterial* * Gene Silencing* * Models, Molecular * RNA Interference * RNA, Archaeal / biosynthesis ... However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and ... Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence- ...
Gene Expression Regulation; Bacterial, Gene Expression Regulation; Enzymologic, Genes; Bacterial, RNA; Bacterial/*genetics, RNA ... Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P.. Dong, H Uppsala universitet ... Endoribonucleases/*genetics, Escherichia coli/enzymology/*genetics/growth & development, Escherichia coli Proteins, Gene ...
Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol. 2005;59:487-517. [PubMed] ... RNA decay in regulation of B. subtilis gene expression. glmS: metabolite-dependent mRNA decay. The B. subtilis glmS gene ... Regulation of bacterial gene expression at the post-transcriptional level has emerged as a major control mechanism, although ... trp operon: recycling of a regulatory RNA-binding protein. A more indirect mechanism for controlling gene expression by RNA ...
Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. ... Identification of small RNAs in Francisella tularensis.. Postic G1, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL. ... RNA extracted from F. tularensis LVS (1) or mutant (2) bacteria in exponential phase was analyzed by Northern blotting using 32 ... A) Total RNA extracted at exponential phase (E), stationary phase (S), high salt concentration (NaCl) or after exposure to ...
Gene Expression Regulation; Bacterial, Models; Genetic, Molecular Sequence Data, Peptides/genetics/*metabolism/toxicity, RNA; ... Bacterial/*genetics, RNA; Messenger/genetics/*metabolism, Research Support; Non-U.S. Govt, Research Support; U.S. Govt; Non-P ... The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Vogel, Jörg Uppsala University, Disciplinary Domain of ... More than 60 small RNAs (sRNA) have been identified in E. coli 1, 2, 3, 4, 5, 6 and 7. The functions of the majority of these ...
Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, thereby affecting ... play a crucial role in the intricate regulation of bacterial gene expression, thereby affecting bacterial pathogenicity. ... The expression of randomly selected novel ncRNAs was confirmed by QPCR. Among the significantly changed ncRNAs, 30 ncRNAs were ... The expression of randomly selected novel ncRNAs was confirmed by QPCR. Among the significantly changed ncRNAs, 30 ncRNAs were ...
Now accepted as fundamentally important players in regulation of gene expression, regulatory RNAs are present in organisms ... 2007) A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional ... 2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 99: ... 2002) Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 16:1696-1706. ...
... play a hitherto unrecognised role in regulation of gene expression. To broaden our knowledge on the function and evolution of ... these molecules, an EU-funded project investigated various classes of regulatory RNAs in different kingdoms.,FP6-LIFESCIHEALTH, ... small nucleolar RNAs and bacterial small RNAs and their role in regulation and modulation of gene expression is just beginning ... Small non-coding RNAs (ncRNAs) play a hitherto unrecognised role in regulation of gene expression. To broaden our knowledge on ...
Gene Expression Regulation, Enzymologic. Genes, Bacterial*. Melanoma / drug therapy, enzymology*, genetics. Mice. N-Glycosyl ... 0/Alkylating Agents; 0/RNA, Messenger; 73-24-5/Adenine; EC 3.2.2.-/N-Glycosyl Hydrolases ... we obtained clones expressing the mRNA of the bacterial tag gene coding for N3-methyladenine-DNA glycosylase I (Gly I), which ... These results suggest that the increased expression of N3-methyladenine-DNA glycosylase is not necessarily a crucial mechanism ...
RNA REGULATED GENE EXPRESSION. Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations. Susan Gottesman ... RNA Worlds: From Lifes Origins to Diversity in Gene Regulation. Subject Area(s): Molecular Biology; Genetics; Biochemistry; ... The X as Model for RNA s Niche in Epigenomic Regulation. Jeannie T. Lee. The Long Arm of Long Noncoding RNAs: Roles as Sensors ... Prologue to the First Edition of The RNA World. James D. Watson. The RNA Worlds in Context. Thomas R. Cech. THE EARLY RNA WORLD ...
... of mRNAs that regulate expression of downstream genes in response to changing concentrations of the second messenger c-di-GMP. ... We discovered three complete c-di-GMP riboswitches (Bc3, Bc4 and Bc5 RNA) with sim … ... c-di-GMP riboswitches are structured RNAs located in the 5-untranslated regions (5-UTRs) ... Gene Expression Regulation* * Gene Expression Regulation, Bacterial * Genes, Reporter* * Nucleic Acid Conformation ...
Small RNA Regulation of Gene Expression in Bacteria. Jennifer A. Doudna, HHMI/University of California, Berkeley, USA Molecular ... Interactions in CRISPR-Mediated Bacterial Immunity. Jin-Wu Nam, Hanyang University, South Korea Short Talk: Long Non-Coding ... It has become apparent that RNA plays a major, but still largely unexplored, role in the regulation of gene expression. It is ... Short Talk: Long Non-Coding RNAs and Their Regulatory Roles in Epigenetic Control of Gene Expression in Plants. ...
Small regulatory RNAs (sRNAs) in eukaryotes and bacteria play an important role in the regulation of gene expression either by ... Quantifying the sequence-function relation in gene silencing by bacterial small RNAs ... Dynamic features of gene expression control by small regulatory RNAs. Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, ... Dynamic features of gene expression control by small regulatory RNAs. Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, ...
... including regulation of translation, gene expression and RNA turnover. The temperature sensitivity of RNA secondary and ... Bacterial RNA thermometers - basic roles and mechanisms. The importance of RNA thermosensing is well illustrated by bacterial ... 2017b). Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates. Nat. Commun. 8, 1570. ... Temperature-modulated regulation by small non-coding RNAs - another mechanism for controlling gene expression and mRNA turnover ...
... in Mollicutes and define the translation apparatus that would be required in a cellular chassis mimicking a minimal bacterial ... proteins are synthesized from the message encoded by mRNA using complex machineries involving many proteins and RNAs. In this ... role in controlling the activity and quality of the translation machinery and the regulation of gene expression by RNA turnover ... Of the original bacterial machinery for translation, only genes coding for the structural RNA (t/r/mRNAs), have been preserved ...
Regulation of gene expression: repression and induction; Operon model; Phage λ and its life cycle; Bacterial genome with ... special reference to E.coli; RNA phages; RNA viruses; Retroviruses; Microbial genomics. ... Section 6- Gene expression in Eukaryotes- Eukaryotic gene organization and expression (Basic principles of signal transduction ... regulation of gene expression, gene mutation and repair, chromosomal aberrations (numerical and structural), transposons. ...
RNA) production is the key to controlling the regulation of bacterial gene expression. Gene expression is the term used to ... The early phase of RNA production may help to control the regulation of bacterial gene expression. ... or RNA molecules.. In bacteria, the RNA is produced using a large protein complex called RNA polymerase (RNAP). The RNAP reads ... The discovery of this new checkpoint in gene expression could be used for the development of new antibiotics. For example, it ...
Positive regulation exploits specific alternative sigma factors to redirect the RNA polymerase enzyme to a subset of selected ... Transcriptional regulation of heat-shock genes can be under either positive or negative control mediated by dedicated ... Sensory biomolecules, also known as thermosensors, include nucleic acids (DNA or RNA) and proteins. Once a stress signal is ... sensory biomolecules sense temperature fluctuations and transduce intercellular signals that coordinate gene expression outputs ...
... play a hitherto unrecognised role in regulation of gene expression. To broaden knowledge on the function and evolution of these ... small nucleolar RNAs, and bacterial small RNAs: Their role in regulation and modulation of gene expression is just beginning to ... Small non-coding RNAs (ncRNAs) play a hitherto unrecognised role in regulation of gene expression. To broaden knowledge on the ... New RNA-based therapeutic strategies for controlling gene expression. February 2, 2012 Small RNA-based nucleic acid drugs ...
regulation of bacterial gene expression is primarily by operons 77 -- on the DNA where RNA polymerase must bind ... When viruses infect new bacterial hosts, delivering viral genome and some bacterial genes ... T or F: The viral genome (a collection of all the genes present) can consist of only a few genes ... is a layer of sugars and proteins on the outer surface of some bacterial cells that forms a sticky layer that can help the cell ...
... are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary ... general features of bacterial small RNA-mRNA interactions? RNA Biol 9:954-965. doi: 10.4161/rna.20294 CrossRefPubMed ... Lustig Y, Wachtel C, Safro M et al (2010) "RNA walk" a novel approach to study RNA-RNA interactions between a small RNA and its ... Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein- ...
... are important elements in the regulation of gene expression for bacteria. Hfq is a bacterial RNA-binding protein that ... RNA based regulation of gene expression. RNA-protein interaction. Thermodynamics of DNA and RNA structural motifs ... Hfq is highly conserved in bacterial phyla and has been shown to be a virulence factor in several bacterial species. The ... Current research is directed at understanding the interaction of the RNA-binding protein Hfq with short regulatory RNAs and its ...
Moreover, regulation by small trans-encoded RNAs has become a focal issue in studies of virulence gene expression of bacterial ... Hansi Kumari, Deepak Balasubramanian, Kalai Mathee, Stress and Environmental Regulation of Gene Expression and Adaptation in ... Expression of phrS requires the oxygen-responsive regulator ANR. Thus, PhrS is the first bacterial sRNA that provides a ... Juan J. Quereda, Pascale Cossart, Regulating Bacterial Virulence with RNA, Annual Review of Microbiology, 2017, 71, 1, 263. ...
ProteinsProteinPromoterGeneticsTranscriptionSynthesisEukaryoticRegulatorsMolecular biologyMechanismNoncoding RNAsRiboswitchesDegradationSequenceRegulatorEnzymeBiochemistryOrganismsBacillusStructuresRibonucleic acidInitiationSpeciesIntergenicSmall regulatoryTRNAConformationBiofilm formationColiPathogenInteractionsMoleculeNucleicChemistrySRNA genesMultiple genesPromotersHeat-shock genesDifferentially expressedRNAPInfectionsRibosomal RNADifferential
- To clarify the molecular mechanism underlying the induction and to exploit this to improve the productivity of recombinant proteins, we tried to identify the regulatory sequence(s) in the 5′ flanking region of the mouse cirp gene. (biomedcentral.com)
- The present novel enhancer permits conditional high-level gene expression at moderately low culture temperatures and could be utilized to increase the yield of recombinant proteins in mammalian cells. (biomedcentral.com)
- Being composed of one consensus sequence-RNA binding domain and a carboxyl-terminal region containing several arginine glycine glycine motifs, it is structurally quite different from bacterial cold shock proteins. (biomedcentral.com)
- Often in cooperation with other transcription factors, Sp proteins regulate the expression of numerous genes implicated in the control of a diverse array of cellular processes, such as cell growth, differentiation, apoptosis, and angiogenesis [ 11 ]. (biomedcentral.com)
- Expression of cold-inducible RNA-binding protein ( cirp , also called cirbp or hnRNP A18 ) is known to be induced in response to mild, but not severe, hypothermia in mammalian cells. (biomedcentral.com)
- Immunohistochemistry and chromatin immunoprecipitation assays demonstrated that more Sp1, but not Sp3, was localized in the nucleus to bind to the cirp regulatory region containing MCRE at 32°C than 37°C. Overexpression of Sp1 protein increased the expression of endogenous Cirp as well as a reporter gene driven by the 5′ flanking region of the cirp gene, and down-regulation of Sp1 had the opposite effect. (biomedcentral.com)
- An introduction to cell structure and synthesis of cell components is provided, followed by detailed discussions of genetics, metabolism, growth, and regulation for anyone wishing to understand the mechanisms underlying cell survival and growth. (mexmat.ru)
- Lecture: developing chemical fundaments of genetics (DNA, RNA), bacterial genetics, gene expression and regulation, pecularities of eukaryotic organisms. (tum.de)
- However, unlike all other such genes, metabolite binding to the glmS UTR does not induce transcription termination or translational regulation but induces autocatalytic cleavage at a 5'-proximal site, leaving a downstream fragment with a 5'-hydroxyl end [ 6 ]. (pubmedcentralcanada.ca)
- Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. (springer.com)
- The RNAP reads the DNA sequence and builds a copy of the RNA by joining nucleotides together - the fundamental building blocks of RNA - during a process called transcription. (medindia.net)
- However, it remained unclear how the production of RNA is also regulated at the stage of early transcription when RNAP has just begun to join together the first few RNA building blocks. (medindia.net)
- To better understand the biological processes regulated by these two transcription factors, we performed RNA sequencing ( RNA-Seq ) on ant ail6 double mutants. (plantphysiol.org)
- The comparison revealed substantial increases in the expression levels of 11 transcription factors that may respond to environmental stimuli. (asm.org)
- An important consequence of this regulatory mechanism is that transcription of a gene can be turned off completely, a distinct advantage for developmental genes. (asm.org)
- As a key enzyme responsible for regulation of gene expression it interprets regulatory signals from the cell and based on these cues RNAP adjusts transcription level of particular genes. (cuni.cz)
- (a) Regulation by cis -encoded RNA, subdivided into signal-mediated folding or unfolding of the translation initiation region (top) or transcription termination/antitermination (bottom). (biomedcentral.com)
- Genome structure and genetic information (Structure of bacterial and eukaryotic genome, genome evolution, genetic code, transcription unit) 3. (muni.cz)
- Genome transcription (Transcription of bacterial and eukaryotic genome, post-transcriptional processing of RNA, mechanisms of RNA splicing) 5. (muni.cz)
- Regulation of gene expression (Control of bacterial and eukaryotic genome expression, induction and repression, operon, transcription factors, posttranscriptional regulatory mechanisms) 7. (muni.cz)
- We studied the statistics of fluctuations of gene expression of HetR, a transcription factor essential for heterocyst differentiation, both under steady-state growth in nitrogen-rich conditions and at different times following nitrogen deprivation, using a chromosomally-encoded translational hetR-gfp fusion. (weizmann.ac.il)
- That means that free α may be involved in transcription regulation affecting expression efficiency of some genes. (jbsdonline.com)
- Excess α enhanced expression efficiency of fepA and decreased fes transcription. (jbsdonline.com)
- Thus, it becomes quite evident that antisense transcription within bacterial genes is far more prevalent, than currently expected. (jbsdonline.com)
- Dr. Yanofsky's research focused on the control of gene expression, specifically the molecular regulatory mechanisms of bacterial transcription. (cshl.edu)
- Investigates the structure, function, and regulation of the bacterial transcription machinery. (rockefeller.edu)
- It locates promoter sequences within the duplex DNA, forms the open promoter complex (RPo) by unwinding the DNA surrounding the transcription start site, initiates the synthesis of an RNA chain, and elongates the RNA processively in an elongation complex (TEC) while translocating itself and the transcription bubble along the DNA template. (rockefeller.edu)
- Darst and his colleagues are seeking a detailed structural and functional understanding of the entire transcription cycle-knowledge that will be essential to explain the fundamental control of gene expression and to target RNAP with small-molecule antibiotics. (rockefeller.edu)
- The researchers are using a combination of x-ray crystallography, cryo-electron microscopy, and other biophysical and biochemical approaches to fill the gaps in our understanding of the bacterial transcription cycle, particularly with regard to the large regulatory complexes and unstable transition states between the cycle's stable states. (rockefeller.edu)
- Controlling the process of transcription is fundamental to gene expression, gene regulation, and development. (nih.gov)
- Because transcription initiation proceeds through multiple steps, this process provides multiple points for regulation. (nih.gov)
- My lab focuses on elucidating these mechanisms of transcription initiation and regulation. (nih.gov)
- Section L:Regulation of transcription in prokaryotes. (slideserve.com)
- Control elements such as an operator sequence, which is a DNA sequence that regulates transcription of the structural genes. (slideserve.com)
- The most common type of regulation involving conditional termination is transcription attenuation, in which the primary regulatory target is an essential element of a single terminator. (asm.org)
- Transcription of NTHi type IV pili was only expressed in co-culture in vitro, and expression could be detected ex vivo in diseased tissue. (elsevier.com)
- However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. (surrey.ac.uk)
- Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. (surrey.ac.uk)
- The transcription of the gene is turned off. (wikipedia.org)
- Promoters are located near the transcription start sites of genes, upstream on the DNA (towards the 5' region of the sense strand ). (wikipedia.org)
- These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression. (wikipedia.org)
- Promoters represent critical elements that can work in concert with other regulatory regions ( enhancers , silencers , boundary elements/ insulators ) to direct the level of transcription of a given gene. (wikipedia.org)
- As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site , where transcription of DNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream). (wikipedia.org)
- In prokaryotes, where splicing is rare, polyadenylation is not nearly as extensive, and there is no physical separation between the sites of RNA synthesis and RNA function, it is likely that RNA decay is a major form of post-transcriptional control. (pubmedcentralcanada.ca)
- This base pairing-dependent regulation stops new synthesis of sugar transporters, and this inhibition is hypothesized to alleviate stress by reducing intracellular accumulation of nonmetabolizable and potentially toxic phosphosugars. (pnas.org)
- During their coevolution with their eukaryotic hosts, mollicutes progressively lost the genes coding for cell-wall synthesis enzymes and for enzymes involved in the synthesis of small metabolites, such as amino acids, nucleotides and lipids that were available in the host. (plos.org)
- In this study, we have identified the small RNA PhrS as an activator of PqsR synthesis, one of the key quorum-sensing regulators in P. aeruginosa . (wiley.com)
- They discovered that the initial RNA synthesis is strongly regulated - a certain sequence of DNA forces the RNAP to pause for several seconds. (medindia.net)
- A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. (asmscience.org)
- An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. (asmscience.org)
- Mechanism and regulation of antibiotic synthesis in Streptomyces. (emory.edu)
- In many eukaryotic organisms, siRNAs and microRNAs (miRNAs) control gene expression at the posttranscriptional level in diverse pathways ( 1 ⇓ - 3 ). (pnas.org)
- Eukaryotic genes are transcribed individually but what are operons? (brainscape.com)
- On the effect of transient expression of mutated eIF2alpha and eIF4E eukaryotic translation initiation factors on reporter gene expression in mammalian cells upon cold-shock. (springer.com)
- Biochemical and structural studies reveal significant functional similarities among bacterial, archaeal, and eukaryotic RNA polymerases. (nih.gov)
- Noncoding RNAs populate virtually all polymer lengths between 20 and 20,000 nucleotides and are found in viruses, prokaryotic cells, and eukaryotic cells (Table 1). (schoolbag.info)
- The past 10 years have seen an unprecedented accumulation of evidence presenting RNAs as ubiquitous regulators rather than merely passive transmitters of genetic information. (europa.eu)
- The mechanism for RNA recognition by ANTAR regulators of gene expression. (nih.gov)
- Bacterial response regulators often display the ability to form dimers or higher oligomers . (nih.gov)
- Virulence gene regulation in Francisella is complex, but transcriptional regulators MglA and SspA have been shown to regulate the expression of approximately 100 genes, including the entire FPI. (asm.org)
- However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. (nih.gov)
- These results suggest that the increased expression of N3-methyladenine-DNA glycosylase is not necessarily a crucial mechanism for the resistance of cells to alkylating agents. (biomedsearch.com)
- Genetic studies revealed a novel mode of regulation by a sRNA, whereby PhrS uses a base-pairing mechanism to activate a short upstream open reading frame to which the pqsR gene is translationally coupled. (wiley.com)
- Mechanism of RNA double helix-propagation at atomic resolution. (gatech.edu)
- Mechanism of RNA Double Helix-Propagation at Atomic Resolution (dagger). (gatech.edu)
- In chapter two, we characterized the mechanism by which F. novicida CRISPR-Cas9 (FnoCas9) represses the expression of bacterial lipoproteins (BLPs), allowing evasion of the host immune system. (hu-berlin.de)
- In this newly-described mechanism, the non-canonical RNA duplex tracrRNA:scaRNA guides FnoCas9 to the DNA target located downstream of the promoter of the BLP-coding genes, causing transcriptional interference. (hu-berlin.de)
- Together, our results define a mechanism for BR-mediated regulation of stem cell quiescence in plants. (sebbm.es)
- Jennifer Doudna , University of California, Berkeley , Howard Hughes Medical Institute and Lawrence Berkeley National Laboratory, and Emmanuelle Charpentier , Helmholtz Center for Infection Research and Umeå University, for harnessing an ancient mechanism of bacterial immunity into a powerful and general technology for editing genomes, with wide-ranging implications across biology and medicine. (wikipedia.org)
- Two recent papers from Pascale Cossart and colleagues [ 6 , 7 ] present a comprehensive microarray analysis of the trans-criptome of Listeria monocytogenes in different conditions, uncovering an unsuspected variety of regulatory roles for noncoding RNAs in controlling changes in gene expression that characterize the transition from saprophytic to pathogenic lifestyle. (biomedcentral.com)
- Subsequent chapters examine riboswitches and ribozymes, establishing what the RNA molecule is capable of alone. (cshlpress.com)
- c-di-GMP riboswitches are structured RNAs located in the 5'-untranslated regions (5'-UTRs) of mRNAs that regulate expression of downstream genes in response to changing concentrations of the second messenger c-di-GMP. (nih.gov)
- Riboswitches are cis-acting RNA elements that modulate gene expression in a highly specialized manner by means of an aptamer domain, an RNA sequence that tightly and selectively binds a given metabolite. (schoolbag.info)
- How this results in depression of gene expression was shown recently by Winkler and colleagues to be due to RNase J1-mediated degradation of the downstream cleavage product ( Fig. 1A ) [ 7 ]. (pubmedcentralcanada.ca)
- Thus, glmS gene expression is regulated by a combination of metabolite-mediated ribozyme cleavage and exonucleolytic degradation. (pubmedcentralcanada.ca)
- These functions modulate a wide range of responses to stresses and other environmental stimuli ( Waters and Storz, 2009 ), including RNA processing, RNA degradation and translation control. (frontiersin.org)
- Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. (weizmann.ac.il)
- We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. (weizmann.ac.il)
- Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. (surrey.ac.uk)
- Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. (nih.gov)
- The DNA sequence of the regions, with the sRNA gene indicated in bold and proposed -10 and -35 boxes underlined, are shown below. (nih.gov)
- Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. (springer.com)
- The ability to predict RNA structure from sequence for structure function studies depends in large measure on thermodynamic parameters of known RNA structural motifs such as internal loops, base mismatches, and base bulges. (gatech.edu)
- At the regulatory level, the developmental program is an ordered, temporal sequence of gene expression events that is coordinated by signaling between cells ( 28 , 33 , 36 ). (asm.org)
- The sequence required for activation of the fts genes by RcsB is shown above the osmC sequence. (asm.org)
- Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. (ucl.ac.uk)
- More than a quarter of all sequence reads mapping outside of ribosomal RNA genes represent non-coding RNA, and the density of reads mapping to intergenic regions was more than two-fold higher than that mapping to annotated coding sequences. (ucl.ac.uk)
- The DNA sequence in the region of the fusion between bla and tRNAArg5 genes is displayed above the plasmid map. (nih.gov)
- To distinguish between the hypotheses described above we constructed a transcriptional fusion between the bla gene and a sequence encoding a tRNA (tRNAArg5) such that both genes become expressed as one single transcript from plasmid pRL11 (Fig. 3). (nih.gov)
- The commercially available, Tn 5 -derived transposome used in this protocol consists of a linear segment of DNA containing an R6K γ replication origin, a gene for kanamycin resistance and two mosaic sequence ends, which serve as transposase binding sites. (jove.com)
- Furthermore, to target a sequence, either for editing or labeling, researchers can make a synthetic RNA strand, known as the guide RNA, that is complementary to the target DNA sequence. (phys.org)
- While CRISPR/Cas9 has some limiting factors, such as off-target cuts or optimizing the PAM sequence, this is a robust method for targeting multiple genes. (phys.org)
- Regulator gene(s) whose products recognize the control elements, for example a repressor which binds to and regulates an operator sequence. (slideserve.com)
- Expression of phrS requires the oxygen-responsive regulator ANR. (wiley.com)
- A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. (asmscience.org)
- The structural genes (any gene other than a regulator) for enzymes involved in a specific biosynthetic pathway whose expression is co-ordinately controlled. (slideserve.com)
- In diverse bacterial species, the global regulator Hfq contributes to post-transcriptional networks that control expression of numerous genes. (pdbj.org)
- The glmS gene codes for glucosamine-6-phosphate (GlcN6P) synthase and expression of the gene is inhibited by the product of the enzyme reaction, GlcN6P. (pubmedcentralcanada.ca)
- The book is thus essential reading for all molecular biologists and biochemists, as well as chemists interested in RNA technology, information storage, or enzyme catalysis. (cshlpress.com)
- What is meant by the "one gene-one enzyme" hypothesis (Beadle and Tatum)? (brainscape.com)
- In its simplest bacterial form, this enzyme comprises four subunits with a total molecular mass of approximately 400 kDa. (rockefeller.edu)
- An enzyme responsible for lactose transport across the bacterial cell wall. (slideserve.com)
- New methods for predicting, detecting and experimentally modifying RNA secondary structure offer promising windows into these fascinating aspects of RNA biochemistry. (biologists.org)
- and (4) the biochemistry and evolution of RNA polyadenylation in various bacterial species, particularly Bacillus. (emory.edu)
- Many professors in the program are recognized for their advanced research in biochemistry, molecular and cell biology, RNA biology and neuroscience. (albany.edu)
- In this article, we focus on regulated RNA decay in the control of gene expression in Gram-positive organisms, with a focus on Bacillus subtilis . (pubmedcentralcanada.ca)
- We describe four examples of this type of regulation from the model Gram-positive organism, Bacillus subtilis , and also cite examples from other Gram-positive organisms. (pubmedcentralcanada.ca)
- Now accepted as fundamentally important players in regulation of gene expression, regulatory RNAs are present in organisms across all domains of life. (pnas.org)
- The experimental work carried out by project partners was geared towards an in-depth understanding of RNA-mediated regulation in a variety of chosen model organisms. (europa.eu)
- This work has implications for understanding how gene expression is controlled in many organisms. (rockefeller.edu)
- This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. (surrey.ac.uk)
- New regulatory small RNAs were identified for both organisms. (surrey.ac.uk)
- DNA and RNA-based approaches are being employed for real-time assessment of contamination levels, bacterial stress responses, and regulation of virulence gene expression in toxigenic Bacillus spp. (bsu.edu)
- In this study, soil samples around campus will be screened for novel bacterial-specific viruses, termed phages, which are specific to toxigenic strains of Bacillus. (bsu.edu)
- The relevant RNA fragments were labelled so that changes in intra- and intermolecular RNA structures can be monitored in real time. (nih.gov)
- The aim of this Commentary is to help acquaint readers with a topic that might be largely unfamiliar - the vast potential of temperature-dependent changes in RNA secondary and tertiary structures (see Glossary) to adaptively modulate the responses of cells to changes in temperature. (biologists.org)
- A model for bacterial gene expression regulation with secondary RNA structures MCCMB 05, 2005, pp. 214 216. (iitp.ru)
- In keeping with such complexity in primary structure, RNA is known to adopt an impressive array of secondary and tertiary structures, and many of these have been elucidated by molecular modeling, biochemical structure determination, and spectroscopic and crystallographic techniques. (schoolbag.info)
- Analyses of these genes suggest that ANT and AIL6 regulate floral organ initiation and growth through modifications to the cell wall polysaccharide pectin. (plantphysiol.org)
- After the initiation of floral organ primordia, these primordia adopt fates as sepals, petals, stamens, or carpels in response to distinct combinations of floral organ identity gene activities as described in the ABCE model (for review, see Krizek and Fletcher, 2005 ). (plantphysiol.org)
- What problem is there for bacterial translation initiation and how is it overcome? (brainscape.com)
- Specific fragments of phage MS2 and fr RNA comprising the translation initiation region of the replicase gene were purified, sequenced and used as template to investigate structural determinants of formation of ribosomal initiation complex. (lza.lv)
- Hfq is highly conserved in bacterial phyla and has been shown to be a virulence factor in several bacterial species. (gatech.edu)
- Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. (nih.gov)
- Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management. (nih.gov)
- Here, we hypothesize that interaction between S. pneumoniae and NTHi mixed-species communities cause a change in bacterial virulence gene expression. (elsevier.com)
- One regulatory gene, FTN_0480 ( fevR , Francisella e ffector of v irulence r egulation), present in all Francisella species, is required for expression of the FPI genes and other genes in the MglA/SspA regulon. (asm.org)
- In the current study, we report that translational repression of the manY and manZ genes by SgrS requires a second binding site located in the manX - manY intergenic region. (pnas.org)
- Heinen TJAJ, Staubach F, Häming D, Tautz D (2009) Emergence of a new gene from an intergenic region. (springer.com)
- Two complementary computational screens, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the intergenic regions IGRs of S. meliloti. (wikipedia.org)
- The mosaic structure of the genes of this class, arising as a result of intergenic recombinations, was discovered. (lza.lv)
- Since strategies used to discover regulatory RNAs were focused primarily on intergenic regions, most aRNAs were found by chance. (jbsdonline.com)
- Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P. (diva-portal.org)
- Connected to this, it is likely that the 5' exonuclease activity of RNase J1 can act directly on the 5' end of native transcripts, once the 5' triphosphate is converted to a 5'-monophosphate by an RNA pyrophosphohydrolase (RppH) activity, similar to the one shown recently by Belasco and colleagues to exist in E. coli [ 8 - 9 ]. (pubmedcentralcanada.ca)
- In a previous study, we demonstrated that the Escherichia coli sRNA SgrS base pairs with a site in the coding region of the first gene of a polycistronic message, manXYZ . (pnas.org)
- Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. (springer.com)
- To cope with adverse conditions, nonsporulating enterobacteria such as Escherichia coli or Salmonella enterica serovar Typhimurium can undergo a global programmed modification of their gene expression pattern, leading to better resistance to a number of chemical and physical stresses such as heat, oxidative agents, or hyperosmotic shock ( 16 , 21 , 22 ). (asm.org)
- The osmC gene of E. coli is a member of this regulon and exhibits a complex regulatory pattern ( 4 , 12 , 15 ). (asm.org)
- Heterologous expression of the putative toxin-encoding mazF(seq) gene imposed growth cessation but not cell death on Escherichia coli. (jove.com)
- In vivo expression of the heat stable (estA) and heat labile (eltB) toxin genes of enterotoxigenic Escherichia coli (ETEC). (gu.se)
- Furthermore, we found that ant ail6 plants have elevated levels of two defense hormones: salicylic acid and jasmonic acid, and show increased resistance to the bacterial pathogen Pseudomonas syringae . (plantphysiol.org)
- Vibrio anguillarum is a bacterial pathogen that causes terminal hemorrhagic septicaemia in marine fish. (diva-portal.org)
- The RNase J-Based RNA Degradosome Is Compartmentalized in the Gastric Pathogen Helicobacter pylori. (pasteur.fr)
- we are also interested in the effect of lactoferrin and lactoperoxidase as a natural antimicrobial against bacterial pathogen growth in raw milk. (bsu.edu)
- This pathogen targets the cytosol of macrophages, where it replicates using the genes in the Francisella pathogenicity island (FPI). (asm.org)
- Overall, our data suggests that Hfq not only promotes strand exchange by binding rapidly to both DsrA and rpoS but also possesses RNA chaperoning properties that facilitates dynamic RNA-RNA interactions. (nih.gov)
- However synthetic interactions between genes are very difficult to identify in population studies because of a lack of statistical power and we fundamentally do not understand how mutations interact to produce phenotypes. (europa.eu)
- Statistical analysis of fluorescence at the individual cell level in wild-type and mutant filaments demonstrates that expression fluctuations of hetR in nearby cells are coupled, with a characteristic spatial range of circa two to three cells, setting the scale for cellular interactions along a filament. (weizmann.ac.il)
- The core of the assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair. (pdbj.org)
- mglA is upregulated inside macrophages 1.5 h postinfection ( 3 ), suggesting that the MglA regulon represents a subset of Francisella genes involved in interactions with macrophages. (asm.org)
- Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. (weizmann.ac.il)
- Their work demonstrated that controlled alterations in RNA structure allow RNA to serve as a regulatory molecule in both bacterial and animal cells. (cshl.edu)
- Our study adds the SOS regulon to the growing list of global regulatory circuits controlled by sRNA genes. (diva-portal.org)
- These files can now be used by the scientific community at large in experiments to search for previously undiscovered sRNA genes and to monitor sRNA gene expression by transcriptome sequencing (RNA-seq). (asm.org)
- Moreover, use of multiple binding sites may be particularly important for coordinating regulation of multiple genes encoded in operons. (pnas.org)
- Summary Most hereditary diseases in humans are genetically complex, resulting from combinations of mutations in multiple genes. (europa.eu)
- The plant-derived compounds TC and EG exert antimicrobial effects on S . Enteritidis PT8 by affecting multiple genes, including those associated with virulence, colonization, cell membrane composition, and transport systems. (frontiersin.org)
- The gene is transcribed from two overlapping promoters, osmCp 1 and osmCp 2 . (asm.org)
- The set of genes with altered expression includes fes encoding enterochelin esterase and fepA encoding outer membrane receptor for ferric enterobactin and colicins B and D. These genes are transcribed from divergent and overlapping promoters fes -P and fepA -P1 plus fepA -P2, respectively, and are inhibited by a repressor Fur. (jbsdonline.com)
- classify promoters in respect to their coding potential and analyze physico-chemical features of expected RNA-products. (jbsdonline.com)
- In the cell nucleus, it seems that promoters are distributed preferentially at the edge of the chromosomal territories, likely for the co-expression of genes on different chromosomes. (wikipedia.org)
- The fact that the RNAP can be simultaneously bound to the DNA and the short piece of RNA for a longer period of time was very surprising, as it contradicts current knowledge,' says Dr. Dulin. (medindia.net)
- Abstrakt Bakteriální RNA polymeráza (RNAP) je proteinový komplex nepostradatelný pro přepis DNA do RNA. (cuni.cz)
- Antibiotics used in treating bacterial infections become ineffective. (medindia.net)
- Antibiotics are used in the treatment of bacterial infections. (medindia.net)
- We are interested in identifying bacterial metabolites and host cell products produced during infection that can be used to identify patients with specific respiratory infections. (louisville.edu)
- This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. (asm.org)
- Gene regulation results in differential gene expression, leading to cell specialization. (prezi.com)